Single-molecule derivation of salt dependent base-pair free energies in DNA
Autor/a
Huguet Casades, Josep Maria
Data de publicació
2010ISSN
1091-6490
Resum
Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our unique energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies, and entropies in conditions not accessible by bulk methodologies.
Tipus de document
Article
Versió del document
Versió publicada
Llengua
English
Matèries (CDU)
57 - Biologia
Paraules clau
Termodinàmica de l'ADN
Descomprimit de l'ADN
Model del veí més proper
Pinces òptiques
Termodinámica del ADN
Descomprimir el ADN
Modelo del vecino más cercano
Pinzas ópticas
DNA thermodynamics
DNA unzipping
Nearest-neighbor model
Optical tweezers
Pàgines
5
Publicat per
National Academy of Sciences
Col·lecció
107; 35
Publicat a
Proceedings of the National Academy of Sciences.
Citació
Huguet Casades, Josep Maria. Single-molecule derivation of salt dependent base-pair free energies in DNA. Proceedings of the National Academy of Sciences, 2010, 107(35), p. 15431-15436. Disponible en: <https://www.pnas.org/doi/full/10.1073/pnas.1001454107>. Fecha de acceso: 18 mar. 2024. DOI: 10.1073/pnas.1001454107
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Drets
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